Understanding ethnic diversity in open dementia neuroimaging data sets.

Ethnic differences in dementia are increasingly recognized in epidemiological measures and diagnostic biomarkers. Nonetheless, ethnic diversity remains limited in many study populations. Here, we provide insights into ethnic diversity in open-access neuroimaging dementia data sets. Data sets comprising dementia populations with available data on ethnicity were included. Statistical analyses of sample and effect sizes were based on the Cochrane Handbook. Nineteen databases were included, with 17 studies of healthy groups or a combination of diagnostic groups if breakdown was unavailable and 12 of mild cognitive impairment and dementia groups. Combining all studies on dementia patients, the largest ethnic group was Caucasian (20 547 participants), with the next most common being Afro-Caribbean (1958), followed by Asian (1211). The smallest effect size detectable within the Caucasian group was 0.03, compared to Afro-Caribbean (0.1) and Asian (0.13). Our findings quantify the lack of ethnic diversity in openly available dementia data sets. More representative data would facilitate the development and validation of biomarkers relevant across ethnicities.

Striatal Dopamine Loss in Early Parkinson's Disease: Systematic Review and Novel Analysis of Dopamine Transporter Imaging.

Background: Neuropathological studies, based on small samples, suggest that symptoms of Parkinson's disease (PD) emerge when dopamine/nigrostriatal loss is around 50-80%. Functional neuroimaging can be applied in larger numbers during life, which allows analysis of the extent of dopamine loss more directly. Objective: To quantify dopamine transporter (DaT) activity by neuroimaging in early PD. Methods: Systematic review and novel analysis of DaT imaging studies in early PD. Results: In our systematic review, in 423 unique cases from 27 studies with disease duration of less than 6 years, mean age 58.0 (SD 11.5) years, and mean disease duration 1.8 (SD 1.2) years, striatal loss was 43.5% (95% CI 41.6, 45.4) contralaterally, and 36.0% (95% CI 33.6, 38.3) ipsilaterally. For unilateral PD, in 436 unique cases, mean age 57.5 (SD 10.2) years, and mean disease duration 1.8 (SD 1.4) years, striatal loss was 40.6% (95% CI 38.8, 42.4) contralaterally, and 31.6% (95% CI 29.4, 33.8) ipsilaterally. In our novel analysis of the Parkinson's Progressive Marker Initiative study, 413 cases had 1436 scans performed. For a disease duration of less than 1 year, age was 61.8 (SD 9.8) years, and striatal loss was 51.2% (95% CI 49.1, 53.3) contralaterally and 39.5% (36.9, 42.1) ipsilaterally, giving an overall striatal loss of 45.3% (43.0, 47.6). Conclusions: Loss of striatal DaT activity in early PD is less at 35-45%, rather than the 50-80% striatal dopamine loss estimated to be present at the time of symptom onset, based on backwards extrapolation from autopsy studies.

The Long and Short of Genome Sequencing: Using a Hybrid Sequencing Strategy to Sequence Oral Microbial Genomes.

Since our chapter on genome sequencing using the GS-FLX pyrosequencer in the First Edition of this book, significant advances have been made in next-generation DNA sequencing (NGS) technology. Not only has the GS-FLX become extinct, but the more recent introduction and establishment of the so-called third-generation DNA sequencers by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) has revolutionized genomics yet again by generating ultra-long (>100,000 basepair) sequence reads concomitant with an incredible reduction in cost per sequenced basepair. Unfortunately, the ultra-high sequence yields of third-generation sequencers are compromised by their inherent sequencing error rates, prompting an alternative sequencing strategy, i.e., a hybrid sequencing strategy, which combines PacBio/ONT primary datasets with complementary datasets generated by mainstream short-read NGS platforms, e.g., Illumina or Ion Torrent. Although the concept of a hybrid sequencing strategy is not new, existing yields and accuracy of ultra-long and short-read sequencing technologies makes such a strategy achievable, resulting in complete genome sequences in one hit. In this chapter, we describe our updated laboratory and bioinformatic protocols that will allow the average research group to obtain complete oral microbial genome sequences assembled from a combination of DNA sequence data generated by NGS and third-generation platforms.

Plaque and Dental Caries Risk in Midlife.

Dental caries is an endogenous microbial community-based disease resulting from an ecological shift from dynamic stability to metabolic imbalance in a consortium of acidogenic and aciduric bacteria comprising the dental plaque biofilm. Participants were members of the Dunedin Multidisciplinary Health and Development Study, a longitudinal investigation of health and behaviour in a cohort born in Dunedin, New Zealand. Oral biofilm samples (collected at age 32 years) from anterior labial supragingival, posterior lingual supragingival, posterior subgingival, and the dorsum of the tongue habitats for 841 participants were analysed using checkerboard DNA-DNA hybridisation (CKB), focussing on 30 ecologically significant bacteria. Associations of CKB data with dental caries at ages 32 and 45 years were assessed using regression modelling, adjusting for potential confounders including sex, xerostomia, and oral hygiene. The putative periodontitis pathobiont Tannerella forsythia (in the anterior supragingival biofilm) was associated with untreated caries at age 32 years. The percentage of total summed cell number counts for two putative periodontitis-associated species (T. forsythia and Micromonas micros) was associated with greater caries experience at age 32 years and the development of new caries between age 32 and 45 years. Additionally, severe caries (3 + cavities) was associated with putative caries pathobionts (Lactobacillus fermentum, Lactobacillus plantarum), periodontitis-associated species, and commensals (M. micros, Campylobacter rectus, Streptococcus mitis biovar I, Streptococcus mitis biovar II) in the subgingival biofilm. Participants with sustained poor oral hygiene through age 32 years not only had greater experience of caries by that age than those with good oral hygiene (fully adjusted incidence risk ratio = 5.10, 95% CI: 3.30, 7.89) but also experienced greater incidence of new caries from age 32 to 45 years (incidence risk ratio = 3.69, 95% CI: 2.62, 5.20). These findings provide evidence in support of the extended caries ecological plaque hypotheses, the polymicrobial aetiology of caries, and the integrated aetiology of dental caries and periodontal diseases. They also underscore the roles of poor oral self-care (particularly over the life course) and xerostomia in the occurrence and progression of caries.

Clinical and Microbiological Evaluation of a Chlorhexidine-Modified Glass Ionomer Cement (GIC-CHX) Restoration Placed Using the Atraumatic Restorative Treatment (ART) Technique.

The aims of this study were to investigate the clinical effectiveness and patient acceptability of a modified glass ionomer cement placed using the atraumatic restorative treatment (ART) technique to treat root caries, and to carry out microbiological analysis of the restored sites. Two clinically visible root surface carious lesions per participant were restored using ART. One was restored with commercial glass ionomer cement (GIC) (ChemFil® Superior, DENTSPLY, Konstonz, Germany) which acted as the control. The other carious root lesion was restored with the same GIC modified with 5% chlorhexidine digluconate (GIC-CHX; test). Patient acceptability and restoration survival rate were evaluated at baseline and after 6 months. Plaque and saliva samples around the test and control restorations were collected, and microbiological analysis for selected bacterial and fungal viability were completed at baseline, and after 1, 3, and 6 months. In total, 52 restorations were placed using GIC and GIC-CHX in 26 participants; 1 patient was lost to follow-up. After reviewing the restorations during their baseline appointments, participants indicated that they were satisfied with the appearance of the restorations (n = 25, 96%) and did not feel anxious during the procedure (n = 24, 92%). Forty-eight percent (n = 12) of the GIC-CHX restorations were continuous with the existing anatomic form as opposed to six for the GIC restorations (24%), a difference which was statistically significant (p = 0.036). There was no statistically significant reduction in the mean count of the tested microorganisms in plaque samples for either type of restorations after 1, 3, or 6 months. Restoration of carious root surfaces with GIC-CHX resulted in higher survival rates than the control GIC. ART using GIC-CHX may therefore be a viable approach for use in outreach dental services to restore root surface carious lesions where dental services are not readily available, and for older people and special needs groups.

Associations of sex, oral hygiene and smoking with oral species in distinct habitats at age 32 years.

The oral microbiome is ecologically diverse, complex, dynamic, and little understood. We describe the microbiota of four oral habitats in a birth cohort at age 32 and examine differences by sex, oral hygiene, and current smoking status, dental caries, and periodontal health. Oral biofilm samples collected from anterior labial supragingival, posterior lingual supragingival, subgingival, and tongue sites of 841 Dunedin Multidisciplinary Health and Development Study members were analysed using checkerboard DNA-DNA hybridization; focusing on 30 ecologically important bacterial species. The four habitats exhibited distinct microbial profiles that differed by sex. Streptococcus gordonii was more dominant in supragingival and tongue biofilms of males; Porphyromonas gingivalis exhibited higher relative abundance in subgingival biofilm of females. Males had higher scores than females for periodontal pathogens at supragingival sites. The relative abundance of several putative caries and periodontal pathogens differed in smokers and non-smokers. With poor oral hygiene significantly higher proportions of Gram-negative facultative anaerobes were present in subgingival biofilm and there were higher scores for the principal components characterised by putative cariogenic and periodontal pathogens at each site. Distinctive microenvironments shape oral biofilms and systematic differences exist by sex, oral hygiene, and smoking status.

Streptococcus salivarius Isolates of Varying Acid Tolerance Exhibit F1F0-ATPase Conservation.

Genes encoding the subunits of the membrane-bound F1F0-ATPase (responsible for exporting protons from the cytoplasm and contributing to acid tolerance) were sequenced for 24 non-mutans streptococci isolated from carious lesions. Isolates, mostly Streptococcus salivarius, displayed a continuum of acid tolerance thresholds ranging from pH 4.55 to 3.39, but amino acid alignments of F1F0-ATPase subunits revealed few non-synonymous substitutions and these were unrelated to acid tolerance. Thus, the F1F0-ATPase is highly-conserved among S. salivarius isolates despite varying acid tolerance thresholds, supporting the contention that acid tolerance is determined by the level of gene/protein expression rather than variation in molecular structure.

A cross-sectional study on the attitudes and perceptions of outpatients towards palliative care at the Hong Kong Queen Mary Hospital Hospice Centre.

BACKGROUND: Palliative care aims to improve the quality of life for patients and their families, by helping them to cope with problems associated with illness. It targets four aspects of health: physical, psychological, social, and spiritual. Most of the current literature on palliative care is limited to the perspectives of health professionals. This study aims to investigate the views of outpatients receiving palliative care at the Hong Kong Queen Mary Hospital Hospice Centre (HKQMHHC), which offers palliative care services to cancer patients. METHODS: This observational cross-sectional study was performed with the completion of a single paper- based original questionnaire over 18 afternoon clinic sessions on Thursdays and Fridays from December 2017 to February 2018 at the HKQMHHC. The questionnaire was designed to examine patients' perspectives; in particular, the Edmonton Symptom Assessment Scale (ESAS) was used to assess their symptoms. Descriptive and univariate analyses were performed. RESULTS: One hundred patients attending HKQMHHC were included in the study. The study revealed that all the mean scores for aspects of care offered at the centre were above 8, on a scale of 0-10 with 0 being extremely inadequate and 10 being extremely adequate. Each respondent was able to identify an average of 1.82 of the 4 aspects of palliative care. Eighty-seven percent of respondents perceived the physical aspect of this care to be of the highest priority. A negative correlation (P<0.05) was found between the extent of symptoms experienced by the patient and their satisfaction towards the services offered. CONCLUSIONS: Patients generally held very positive attitudes, reflecting that the services sufficiently met their needs. However, owing to their rather limited knowledge, this may have restricted their perspectives to a largely superficial level, as many discerned palliative care to be simply targeting physical health with medical consultations. Considering the implications of the results, the addition of accessibility and education components to Hong Kong's current system of palliative care is crucial in the betterment of such services for patients. There should also be increased local coverage of palliative care services to facilitate convenience of access. With reference to the World Health Organisation (WHO) palliative care model, the inclusion of a continued spectrum of services, such as physical and mental health activities and psychosocial counselling, should be reinforced throughout the progression of disease so as to better help patients to cope with illness. The discovery of the relationship between extent of symptoms experienced and patients' satisfaction towards services provided is a new direction for further study.

A TaqMan™-based quantitative PCR screening assay for the probiotic Streptococcus salivarius K12 based on the specific detection of its megaplasmid-associated salivaricin B locus.

In order to assess the colonization efficacy of the oral probiotic Streptococcus salivarius K12, a rapid method for specific detection and enumeration of the strain was developed. Here, we describe a two-step TaqMan™ quantitative PCR assay using primer-probe combinations targeting genes of the locus encoding the lantibiotic bacteriocin salivaricin B.

Oral bacteriome of HIV-1-infected children from Rio de Janeiro, Brazil: Next-generation DNA sequencing analysis.

BACKGROUND AND AIM: This study compared the oral bacteriome between HIV-1-infected and non-HIV-1-infected Brazilian children/teenagers. METHODS: Whole saliva, biofilm from the dorsal surface of the tongue and biofilm from supragingival and subgingival sites were collected from 27 HIV-1-infected and 30 non-HIV-1-infected individuals. Bacterial genomic DNA was extracted and 16S rRNA genes were sequenced using next-generation sequencing technology (Ion Torrent). RESULTS: In the supragingival biofilm, the phylum Firmicutes and genus Streptococcus sp. were more frequent in HIV-1-infected (95% and 78%, respectively) than in non-HIV-1-infected individuals (40% and 24%, respectively). In the subgingival biofilm of HIV-infected participants, the relative abundance of the Veillonella sp. and Prevotella sp. genera were higher than in non-HIV-1-infected participants. On the tongue, the genera with greater relative abundance in HIV-1-infected individuals were Neisseria sp. (21%). In saliva, the difference of the genus Prevotella sp. between non-HIV-1-infected and HIV-1-infected individuals was 15% and 7%, respectively. The Chao index revealed an increase in the richness of both sub- and supragingival biofilms in the HIV-1-infected samples compared with non-HIV-1-infected samples. CONCLUSION: HIV-1-infected children/teenagers have a higher frequency of the phyla Firmicutes and genus Streptococcus, and their oral microbiome shows more complexity than that of non-HIV-1-infected children/teenagers.

Three Bacteriocin Peptides from a Lactic Acid Bacterium Weissella confusa MBF8-1 with Spermicidal Activity.

BACKGROUND: The development of antibiotic resistance amongst bacterial pathogens and a population explosion, e.g. in countries such as Indonesia, are two issues the world is facing today. These issues have stimulated interest in the development of new antimicrobial therapeutic agents and contraceptive strategies, such as novel spermicides. Bacteriocins, which are bacterially-derived antimicrobial peptides, may fulfill some of the criteria for these new agents. METHODS: Weissella confusa MBF8-1, originally isolated from a homemade soy product, exhibits antibacterial activity that was subsequently found to be plasmid-encoded, presumably by three peptides Bac1, Bac2 and Bac3. In the present study, we tested cell-free MBF8-1 bacteriocin preparations and chemically-synthesized versions of Bac1, Bac2 and Bac3 peptides for (i) its antibacterial activity against the indicator bacterium Leuconostoc mesenteroides and (ii) its ability to affect the motility of spermatozoa. Nisin, a known lantibiotic bacteriocin, was used as the control. RESULTS: Here, we demonstrate that synthetic Bac1, in combination with synthetic Bac2, was sufficient to inhibit the growth of L. mesenteroides and affect sperm motility. However, the presence of all three synthetic peptides, s-Bac1, s-Bac2 and s-Bac3, was required for full potency. CONCLUSION: In summary, the bacteriocin-like peptides of W. confusa MBF8-1 have the potential to be developed as a narrow-spectrum antimicrobial agent and a novel spermicidal agent.

Oral probiotics reduce halitosis in patients wearing orthodontic braces: a randomized, triple-blind, placebo-controlled trial.

Orthodontic braces can impede oral hygiene and promote halitosis. The aim of the study was to investigate the effect of the oral probiotic Streptococcus salivarius M18 on oral hygiene indices and halitosis in patients wearing orthodontic braces. The study was a prospective, randomized, triple-blind, placebo-controlled trial. Patients undergoing fixed orthodontic treatment were randomly allocated to a probiotic group (n = 32) and a placebo group (n = 32). Patients consumed 2 lozenges d-1 for one month. Assessments were taken at baseline, at the end of the intervention, and at a 3 month follow-up. The outcome measures were plaque index (PI), gingival index (GI) and halitosis-causing volatile sulfur compound (VSC) levels. The dental biofilms before and after the intervention were analyzed utilizing next-generation sequencing of bacterial 16S rRNA genes. PI and GI scores were not significantly influenced by the probiotic intervention (intervention × time: p > 0.05). The level of VSCs decreased significantly in both the probiotic group (VSC reduction = -8.5%, 95%CI = -7.4% to -9.1%, p = 0.015) and the placebo group (-6.5%, 95%CI = -6.0% to -7.4%, p = 0.039) after 1 month intervention. However, at the 3 month follow-up, the VSC levels in the placebo group returned to baseline levels whereas those in the probiotic group decreased further (-10.8%, 95%CI = -10.5% to -12.9%, p = 0.005). Time, but not treatment, was associated with the decrease in microbial community alpha diversity and a modest effect on beta diversity. Oral probiotic S. salivarius M18 reduced the level of halitosis in patients with orthodontic braces, but had minimal effects on PI, GI and dental biofilm microflora.

Bacteriocin-like inhibitory substance (BLIS) activity of Streptococcus macedonicus MBF10-2 and its synergistic action in combination with antibiotics.

OBJECTIVE: To characterize the bacteriocin-like inhibitory-substances (BLIS) activity of Streptococcus macedonicus MBF10-2 [named BLIS(MBF10-2)], a bacteriocinogenic strain isolated from an Indonesian tofu byproduct. METHODS: BLIS(MBF10-2) was obtained by culturing the bacterium, and standard deferred antagonism assays were used to demonstrate its activity. The antibacterial testing of fractions collected by filtration using 3-30 kDa cut-off membrane sizes were carried out by performing well diffusion method. RESULTS: The growth of Micrococcus luteus, Streptococcus pyogenes, Lactococcus lactis, Leuconostoc mesenteroides and Weissella confusa were inhibited by BLIS(MBF10-2). Interestingly, BLIS-containing fractions obtained from sequential application on ultrafiltration membranes indicated that this bacterium Streptococcus macedonicus MBF10-2 could produces at least two antimicrobial peptides activities, one of which is likely to be a lantibiotic peptide. Potential synergistic activity against certain Gram-positive (but not Gram-negative) species when partnered with antibiotics (ampicillin, tetracycline or kanamycin) were observed. CONCLUSION: Combination of some BLIS(MBF10-2) active fractions with antibiotics (ampicillin, tetracycline or kanamycin) could demonstrate synergistic activities against certain Gram-positive species.

Draft Genome Sequence of Weissella confusa MBF8-1, a Glucansucrase- and Bacteriocin-Producing Strain Isolated from a Homemade Soy Product.

We report here the draft genome sequence of Weissella confusa MBF8-1, an isolate from a homemade fermented soybean product that produces sucrases and exhibits antibacterial (bacteriocin) activity. The draft genome of W. confusa MBF8-1 comprises a 2.2-Mbp chromosome and a 17.8-kbp bacteriocin-encoding plasmid. Two putative glucansucrase genes were also identified.

Tackling the health impacts of climate change in the twenty-first century.

The turn of the twenty-first century has borne witness to the seemingly relentless march of climate change, with global mean temperatures and sea levels projected to rise significantly in the near future. Despite considerable improvements in healthcare, mortality rates and life expectancy worldwide over the past few decades, there is increasing evidence postulating the potentially adverse impacts of environmental alterations on health in more ways than one. These not only involve direct and indirect climatic-related health impacts, but also those modulated by human aspects. Undeniably, there is a pressing need to recognize these issues and come up with appropriate solutions to address them as much as possible. Fortunately, this has led to the development of a wide range of measures encompassing both adaptation and mitigation strategies, alongside the recent Paris accords which highlight renewed global resolve in tackling these challenges in a collaborative and coordinated manner. However, progress has been relatively muted, and whether these prove to be the turning point remains very much to be seen. Nonetheless, taking the above into consideration, there is little doubt about the gravity of the situation, and that much more needs to be done to integrate and bring society forward in this new era.

Identification and sequence analysis of pWcMBF8-1, a bacteriocin-encoding plasmid from the lactic acid bacterium Weissella confusa.

Members of the Gram-positive lactic acid bacteria (LAB) are well-known for their beneficial properties as starter cultures and probiotics. Many LAB species produce ribosomally synthesized proteinaceous antibiotics (bacteriocins). Weissella confusa MBF8-1 is a strain isolated from a fermented soybean product that not only produces useful exopolysaccharides but also exhibits bacteriocin activity, which we call weissellicin MBF. Here, we show that bacteriocin production by W. confusa MBF8-1 is specified by a large plasmid, pWcMBF8-1. Plasmid pWcMBF8-1 (GenBank accession number KR350502), which was identified from the W. confusa MBF8-1 draft genome sequence, is 17 643 bp in length with a G + C content of 34.8% and contains 25 open reading frames (ORFs). Six ORFs constitute the weissellicin MBF locus, encoding three putative double-glycine-motif peptides (Bac1, Bac2, Bac3), an ABC transporter complex (BacTE) and a putative immunity protein (BacI). Two ORFs encode plasmid partitioning and mobilization proteins, suggesting that pWcMBF8-1 is transferable to other hosts. To the best of our knowledge, plasmid pWcMBF8-1 not only represents the first large Weissella plasmid to be sequenced but also the first to be associated with bacteriocin production in W. confusa.

Salivaricin E and abundant dextranase activity may contribute to the anti-cariogenic potential of the probiotic candidate Streptococcus salivarius JH.

Dental caries is an infectious disease that is continuing to increase in prevalence, reducing the quality of life for millions worldwide as well as causing considerable expense, with an estimated US$108 billion spent on dental care in the USA each year. Oral probiotics are now being investigated to determine whether they could play a role in the prevention and treatment of this disease. Streptococcus salivarius strain JH is a potential probiotic candidate that produces multiple proteinaceous antimicrobials (bacteriocins), the inhibitory spectrum of which includes Streptococcus mutans, one of the principal causative agents of dental caries. The genome of strain JH has previously been shown to contain the biosynthetic loci for the bacteriocins salivaricin A3, streptin and streptococcin SA-FF22. Here we show that strain JH also produces salivaricin E, a 32 aa lantibiotic with a mass of 3565.9 Da, which is responsible for the inhibition of S. mutans growth. In addition, strain JH was shown to produce dextranase, an enzyme that hydrolyses (1 → 6)-α-D-glucosidic linkages, at levels higher than any other S. salivarius tested. In vitro testing showed that partial hydrolysis of the exopolymeric substances of S. mutans, using strain JH dextranase, improved the anti-S. mutans inhibitory activity of the lytic bacteriocin, zoocin A. The multiple bacteriocin and dextranase activities of strain JH support its candidature for development as an oral probiotic.

Developing oral probiotics from Streptococcus salivarius.

Considerable human illness can be linked to the development of oral microbiota disequilibria. The predominant oral cavity commensal, Streptococcus salivarius has emerged as an important source of safe and efficacious probiotics, capable of fostering more balanced, health-associated oral microbiota. Strain K12, the prototype S. salivarius probiotic, originally introduced to counter Streptococcus pyogenes infections, now has an expanded repertoire of health-promoting applications. K12 and several more recently proposed S. salivarius probiotics are now being applied to control diverse bacterial consortia infections including otitis media, halitosis and dental caries. Other potential applications include upregulation of immunological defenses against respiratory viral infections and treatment of oral candidosis. An overview of the key steps required for probiotic development is also presented.